The difference between ptor.findElement and element is that the first should be used pages without Angular while the second is used on pages with Angular. This is related to how protractor syncs with Angular. The first returns a WebDriver WebElement, the second returns a Protractor ElementFinder.
However to address your question directly, there is no difference between the locators returned by by.css and protractor.By.css.
The two are equivalent. The object referenced by the global by object is the same as the the object referenced by protractor.By.
From Protractor's runner.js:
global.by = global.By = protractor.By;
There are two versions of the API. The old version used protractor.By, whereas the new version uses by. You may often see the old style but if you are in doubt, you can use the new style and be sure nothing unexpected will happen.